OTUD5 p.Pro563=
c.1689A>G · rs1557046703 · VCV2660489
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00056%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.6 | GERP -3.2, phastCons 1 |
| Overall | ||
| CADD | 8.07 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00056%
European (non-Finnish) · 5/893,406 alleles
Filtering AF
0.000164%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000119%
Overall
0.000414%
5/1,208,886 alleles · very rare
exomes 5/1,096,108 · genomes 0/112,778 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- OTUD5
- Protein
- p.Pro563=
- Coding
- c.1689A>G
- MANE Select
- NM_001136157
- dbSNP
- rs1557046703
- Type
- single nucleotide variant
- Location
- chrX:48923186 (GRCh38)
- Structure
- AlphaFold pLDDT 66.15 · 3 PDB
Similar variants
- OTUD5 p.Pro563Thr Uncertain significance ⚠ same residue
- OTUD5 p.Pro563_Asp564insPro Uncertain significance ★ same residue
- OTUD5 p.Arg515Trp Likely pathogenic ★★ ⚠ same type
- OTUD5 p.Ala487Val Uncertain significance ★★ ⚠ same type
- OTUD5 p.Cys143Ser Uncertain significance ★★ same type
- OTUD5 p.Gln217Arg Uncertain significance ★★ ⚠ same type
- OTUD5 p.Met468Thr Uncertain significance ★★ ⚠ same type
- OTUD5 p.Pro20Gln Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/otud5-p-pro563 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown